getCrisprGuides {RareVariantVis} | R Documentation

## Retrieve CRISPR/Cas9 guides.

### Description

Function checks whether a guideRNA can be found that overlaps given SNP. Returns sequence of the guideRNA with the variant marked with the lowercase letters. When multiple guideRNAs are possible for given SNP, guideRNA with the variant closest to the PAM site is being selected.

### Arguments

`df` | A data frame, preferably out from chromosomeVis.
`genome` | A object of the BSGenome, by default BSgenome.Hsapiens.UCSC.hg19.
`gsize` | Prefered size of the guideRNA, by default, standard 23 is used.
`PAM` | Prefered Protospacer Adjecent Motif "PAM", short motif that has to be found on the 5' end of the guideRNA, by default, Cas9 is used "GG".
`PAM_rev` | Prefered Protospacer Adjecent Motif "PAM", short motif that has to be found on the reverse strand, by default, Cas9 is used "CC". This is checked only when no guideRNA is found on the forward strand.

### Value

`character vector` | Vector of guideRNAs, when no guideRNA was found for the forward strand, reverse strand is checked, when no guideRNA is found NA is returned.

### Author(s)

Kornel Labun

### Examples

    file <- system.file("extdata", "RareVariants_CoriellIndex_S1.txt",
        package = "RareVariantVis")
    df <- read.delim(file, stringsAsFactors = FALSE)
    getCrisprGuides(df)

[Package RareVariantVis version 2.16.0 Index]